Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
13,530 results • Page
2 of 271
Sort: Views
Rank
Views
Votes
Replies
48
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 12 weeks ago by
Picasa
▴ 640 • written 7.5 years ago by
ZheFrench
▴ 570
121
votes
35
replies
43k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 11 months ago by
Ram
43k • written 6.9 years ago by
ropolocan
▴ 810
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 7 months ago by
zx8754
11k • written 11.3 years ago by
henryvuong
▴ 810
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 7 months ago by
Joel Wallenius
▴ 210 • written 10.2 years ago by
pristanna
▴ 750
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 7 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing
fastq
updated 5 months ago by
Pierre Lindenbaum
161k • written 14.0 years ago by
Zach Stednick
▴ 660
121
votes
33
replies
39k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by
carlopecoraro2
★ 2.5k • written 10.7 years ago by
Eric Normandeau
11k
6
votes
25
replies
38k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 10 months ago by
13554221497
• 0 • written 6.1 years ago by
ARich
▴ 130
23
votes
4
replies
38k
views
bcftools compressing and indexing vcf files
sequence
bcftools
vcf
index
updated 5 months ago by
GenoMax
141k • written 5.6 years ago by
Inquisitive8995
▴ 270
19
votes
10
replies
38k
views
Ensembl ID to Gene Symbol
gene-symbol
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by
Axzd
▴ 70 • written 9.8 years ago by
onter
▴ 170
13
votes
6
replies
37k
views
generating genome indexes with STAR
RNA-Seq
STAR
updated 9 months ago by
DareDevil
★ 4.3k • written 7.8 years ago by
snp87
▴ 80
10
votes
5
replies
37k
views
How to compare 2 VCF files
vcf
SNP
updated 10 months ago by
Ram
43k • written 9.9 years ago by
Parimala Devi
▴ 100
80
votes
21
replies
36k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by
kathryn.jacksonjones
• 0 • written 10.0 years ago by
M K
▴ 660
21
votes
8
replies
36k
views
8 follow
Merging/Concatenating Vcf Files
vcftools
snp
indel
updated 8 months ago by
Bioinformatics_NewComer
▴ 330 • written 11.7 years ago by
bioinfo
▴ 830
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
141k • written 3.7 years ago by
lavinia.gordon
▴ 160
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq
macs
ChIP-Seq
peaks
updated 10 months ago by
Ram
43k • written 7.7 years ago by
igor
13k
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing
duplicates
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
161k
33
votes
10
replies
35k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq
ensembl
updated 9 months ago by
Ram
43k • written 9.8 years ago by
pwg46
▴ 540
197
votes
27
replies
34k
views
20 follow
Forum:
Bioinformatics Cartoon
bioinformatics
updated 9 months ago by
Ram
43k • written 12.3 years ago by
Maxime Lamontagne
★ 2.3k
20
votes
10
replies
34k
views
6 follow
read depth using samtools
depth
samtools
updated 7 months ago by
Sachin
▴ 10 • written 5.3 years ago by
LimMo
▴ 30
13
votes
12
replies
34k
views
Estimating Insert Size From Paired End Data.
picard
alignment
paired-end
updated 6 months ago by
Ram
43k • written 10.2 years ago by
GouthamAtla
12k
39
votes
23
replies
34k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 7 months ago by
s.w.vanderlaan
▴ 40 • written 2.8 years ago by
Michal Nevo
▴ 130
28
votes
11
replies
34k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools
strand
updated 3 months ago by
shaoqian ma
• 0 • written 12.4 years ago by
Gregor Rot
▴ 540
42
votes
16
replies
34k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 7 months ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
chparada
▴ 70
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
67
votes
15
replies
33k
views
14 follow
Rna-Seq Pipeline
pipeline
next-gen-sequencing
rna
rna-seq
updated 11 months ago by
Ram
43k • written 13.9 years ago by
brentp
24k
298
votes
122
replies
33k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 7 months ago by
jena
▴ 290 • written 13.8 years ago by
Eric Normandeau
11k
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 7 weeks ago by
nickp60
▴ 60 • written 7.8 years ago by
andrew.j.skelton73
6.5k
36
votes
11
replies
32k
views
6 follow
Sjdboverhang Option In Star
updated 9 months ago by
Kermit
▴ 90 • written 10.2 years ago by
Martombo
★ 3.1k
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 4 months ago by
asalimih
▴ 60 • written 9.7 years ago by
mike
▴ 90
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter
sequence
human
genome
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Yuri
★ 1.7k
20
votes
9
replies
32k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart
r
bioconductor
updated 11 months ago by
Kevin Blighe
87k • written 11.8 years ago by
sthait
▴ 120
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
79
votes
86
replies
31k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 10 months ago by
Ram
43k • written 7.4 years ago by
Brian Bushnell
20k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner
snp
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
72
votes
71
replies
31k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot
bioconductor
ggplot2
ggrepel
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Kevin Blighe
87k
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 15 days ago by
Jeremy Leipzig
22k • written 10.4 years ago by
14134125465346445
★ 3.6k
28
votes
16
replies
31k
views
11 follow
How Do I Convert From Bed Format To Gff Format?
gff
galaxy
bed
updated 6 months ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
14
votes
8
replies
31k
views
NarrowPeak format of ChiP-seq
ChIP-Seq
tag-density
updated 10 months ago by
minakshiboruahassam
• 0 • written 9.9 years ago by
liu4gre
▴ 210
130
votes
19
replies
31k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq
alignment
next-gen
R
assembly
updated 3 months ago by
Ram
43k • written 4.6 years ago by
WUSCHEL
▴ 750
4
votes
9
replies
31k
views
8 follow
How To Get Chromosome Position Given Rs Number?
snp
chromosome
position
updated 5 months ago by
GenoMax
141k • written 10.4 years ago by
chrismas05
• 0
23
votes
12
replies
30k
views
9 follow
Extract Alignment From Very Large Bam File
bam
updated 3 months ago by
Ram
43k • written 11.9 years ago by
Plantae
▴ 390
25
votes
11
replies
30k
views
9 follow
Bed For Agilent Sureselect All Exon Kits ?
bed
exome
agilent
next-gen
written 11.4 years ago by
Pierre Lindenbaum
161k
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp
amino-acids
updated 3 months ago by
gernophil
▴ 80 • written 12.3 years ago by
Preethi
▴ 110
52
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 9 months ago by
DareDevil
★ 4.3k • written 10.7 years ago by
user
▴ 940
13
votes
3
replies
29k
views
What is the difference between blastx and tblastn?
assembly
blast
ncbi
sequence
updated 10 months ago by
Ram
43k • written 4.8 years ago by
Kumar
▴ 120
19
votes
9
replies
28k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis
RNA-Seq
ngs
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Arindam Ghosh
▴ 510
16
votes
6
replies
28k
views
7 follow
How To Convert Bed Format To Gtf?
gtf
bed
updated 8 months ago by
alejandrogzi
▴ 120 • written 11.2 years ago by
ftp
▴ 140
13,530 results • Page
2 of 271
Recent Votes
Interested in Spatial Omics?
Answer: Seurat merge and batch correction
Answer: Seurat merge and batch correction
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Recent Locations •
All
Australia,
4 minutes ago
India,
4 minutes ago
United States,
5 minutes ago
India,
8 minutes ago
Berlin,
10 minutes ago
Japan,
10 minutes ago
United States,
11 minutes ago
Recent Awards •
All
Popular Question
to
subhiksha
▴ 30
Popular Question
to
v.berriosfarias
▴ 140
Popular Question
to
AdviceSeeker
• 0
Great Question
to
Ann
★ 2.4k
Scholar
to
marco.barr
▴ 80
Popular Question
to
Kash
▴ 110
Scholar
to
GenoMax
141k
Recent Replies
Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Traffic: 1918 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6